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libsbml.Deletion Class Reference
Inheritance diagram for libsbml.Deletion:
[legend]

Detailed Description

{comp}

comp Implementation of the Deletion construct from the “comp” package.

The Deletion class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to allow elements of submodels to be removed before instantiation. The Deletion object class is used to define a deletion operation to be applied when a submodel instantiates a model definition. Deletions may be useful in hierarchical model composition scenarios for various reasons. For example, some components in a submodel may be redundant in the composed model, perhaps because the same features are implemented in a different way in the new model. Deletions function as follows. When the Model to which the Submodel object refers (via the 'modelRef' attribute) is read and processed for inclusion into the composed model, each Deletion object identifies an object to remove from that Model instance. The resulting submodel instance consists of everything in the Model object instance minus the entities referenced by the list of Deletion objects.

As might be expected, deletions can have wide-ranging implications, especially when the object deleted has substantial substructure, as in the case of reactions. The following are rules regarding deletions and their effects.

  • An object that has been deleted is considered inaccessible. Any element that has been deleted (or replaced) may not be referenced by an SBaseRef object.
  • If the deleted object has child objects and other structures, the child objects and substructure are also considered to be deleted.
  • It is not an error to delete explicitly an object that is already deleted by implication (for example as a result of the second point above). The resulting model is the same.
  • If the deleted object is from an SBML namespace that is not understood by the interpreter, the deletion must be ignored—the object will not need to be deleted, as the interpreter could not understand the package. If an interpreter cannot tell whether a referenced object does not exist or if exists in an unparsed namespace it may produce a warning.

The Deletion object class is subclassed from SBaseRef, and reuses all the machinery provided by SBaseRef. In addition, it defines two optional attributes, 'id' and 'name'. The 'id' attribute can be used to give an identifier to a given deletion operation. The identifier has no mathematical meaning, but it may be useful for creating submodels that can be manipulated more directly by other submodels. (Indeed, it is legitimate for an enclosing model definition to delete a deletion!)

The optional 'name' attribute is provided on Deletion for the same reason it is provided on other elements that have identifiers; viz., to provide for the possibility of giving a human-readable name to the object. The name may be useful in situations when deletions are displayed to modelers.

Public Member Functions

def addCVTerm
 
def appendAnnotation
 
def appendNotes
 
def clearReferencedElement
 
def clone
 
def createSBaseRef
 
def disablePackage
 
def enablePackage
 
def getAncestorOfType
 
def getAnnotation
 
def getAnnotationString
 
def getColumn
 
def getCVTerm
 
def getCVTerms
 
def getElementByMetaId
 
def getElementBySId
 
def getElementName
 
def getId
 
def getIdRef
 
def getLevel
 
def getLine
 
def getListOfAllElements
 
def getListOfAllElementsFromPlugins
 
def getMetaId
 
def getMetaIdRef
 
def getModel
 
def getModelHistory
 
def getName
 
def getNamespaces
 
def getNotes
 
def getNotesString
 
def getNumCVTerms
 
def getNumPlugins
 
def getNumReferents
 
def getPackageName
 
def getPackageURI
 
def getPackageVersion
 
def getParentModel
 
def getParentSBMLObject
 
def getPlugin
 
def getPortRef
 
def getPrefix
 
def getReferencedElement
 
def getReferencedElementFrom
 
def getResourceBiologicalQualifier
 
def getResourceModelQualifier
 
def getSBaseRef
 
def getSBMLDocument
 
def getSBOTerm
 
def getSBOTermAsURL
 
def getSBOTermID
 
def getTypeCode
 
def getUnitRef
 
def getURI
 
def getVersion
 
def hasRequiredAttributes
 
def hasValidLevelVersionNamespaceCombination
 
def isPackageEnabled
 
def isPackageURIEnabled
 
def isPkgEnabled
 
def isPkgURIEnabled
 
def isSetAnnotation
 
def isSetId
 
def isSetIdRef
 
def isSetMetaId
 
def isSetMetaIdRef
 
def isSetModelHistory
 
def isSetName
 
def isSetNotes
 
def isSetPortRef
 
def isSetSBaseRef
 
def isSetSBOTerm
 
def isSetUnitRef
 
def matchesRequiredSBMLNamespacesForAddition
 
def matchesSBMLNamespaces
 
def performDeletion
 
def removeFromParentAndDelete
 
def removeTopLevelAnnotationElement
 
def renameMetaIdRefs
 
def renameSIdRefs
 
def renameUnitSIdRefs
 
def replaceTopLevelAnnotationElement
 
def saveReferencedElement
 
def setAnnotation
 
def setId
 
def setIdRef
 
def setMetaId
 
def setMetaIdRef
 
def setModelHistory
 
def setName
 
def setNamespaces
 
def setNotes
 
def setPortRef
 
def setSBaseRef
 
def setSBOTerm
 
def setUnitRef
 
def toSBML
 
def toXMLNode
 
def unsetAnnotation
 
def unsetCVTerms
 
def unsetId
 
def unsetIdRef
 
def unsetMetaId
 
def unsetMetaIdRef
 
def unsetModelHistory
 
def unsetName
 
def unsetNotes
 
def unsetPortRef
 
def unsetSBaseRef
 
def unsetSBOTerm
 
def unsetUnitRef
 

Member Function Documentation

def libsbml.SBase.addCVTerm (   self,
  args 
)
inherited

Python method signature(s):

addCVTerm(SBase self, CVTerm term, bool newBag=False)   int
addCVTerm(SBase self, CVTerm term)   int

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.appendAnnotation (   self,
  args 
)
inherited

Python method signature(s):

appendAnnotation(SBase self, XMLNode annotation)   int
appendAnnotation(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendAnnotation(XMLNode annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
appendAnnotation(string annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.appendNotes (   self,
  args 
)
inherited

Python method signature(s):

appendNotes(SBase self, XMLNode notes)   int
appendNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendNotes(string notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBaseRef.clearReferencedElement (   self)
inherited

Python method signature(s):

clearReferencedElement(SBaseRef self)

Removes the saved referenced element, if it had been saved earlier.

def libsbml.Deletion.clone (   self)

{comp}

comp Implementation of the Deletion construct from the “comp” package.

The Deletion class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to allow elements of submodels to be removed before instantiation. The Deletion object class is used to define a deletion operation to be applied when a submodel instantiates a model definition. Deletions may be useful in hierarchical model composition scenarios for various reasons. For example, some components in a submodel may be redundant in the composed model, perhaps because the same features are implemented in a different way in the new model. Deletions function as follows. When the Model to which the Submodel object refers (via the 'modelRef' attribute) is read and processed for inclusion into the composed model, each Deletion object identifies an object to remove from that Model instance. The resulting submodel instance consists of everything in the Model object instance minus the entities referenced by the list of Deletion objects.

As might be expected, deletions can have wide-ranging implications, especially when the object deleted has substantial substructure, as in the case of reactions. The following are rules regarding deletions and their effects.

  • An object that has been deleted is considered inaccessible. Any element that has been deleted (or replaced) may not be referenced by an SBaseRef object.
  • If the deleted object has child objects and other structures, the child objects and substructure are also considered to be deleted.
  • It is not an error to delete explicitly an object that is already deleted by implication (for example as a result of the second point above). The resulting model is the same.
  • If the deleted object is from an SBML namespace that is not understood by the interpreter, the deletion must be ignored—the object will not need to be deleted, as the interpreter could not understand the package. If an interpreter cannot tell whether a referenced object does not exist or if exists in an unparsed namespace it may produce a warning.

The Deletion object class is subclassed from SBaseRef, and reuses all the machinery provided by SBaseRef. In addition, it defines two optional attributes, 'id' and 'name'. The 'id' attribute can be used to give an identifier to a given deletion operation. The identifier has no mathematical meaning, but it may be useful for creating submodels that can be manipulated more directly by other submodels. (Indeed, it is legitimate for an enclosing model definition to delete a deletion!)

The optional 'name' attribute is provided on Deletion for the same reason it is provided on other elements that have identifiers; viz., to provide for the possibility of giving a human-readable name to the object. The name may be useful in situations when deletions are displayed to modelers. Python method signature(s):

clone(Deletion self)   Deletion

Creates and returns a deep copy of this Deletion object.

Returns
a (deep) copy of this Deletion object
def libsbml.SBaseRef.createSBaseRef (   self)
inherited

Python method signature(s):

createSBaseRef(SBaseRef self)   SBaseRef

Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef.

Returns
the newly created SBaseRef object instance.
def libsbml.SBase.disablePackage (   self,
  args 
)
inherited

Python method signature(s):

disablePackage(SBase self, string pkgURI, string pkgPrefix)   int

Disables the given SBML Level 3 package on this object.

This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

import sys
import os.path
from libsbml import *

# We read in an SBML L3V1 model that uses the 'comp' package namespace
doc = readSBML('sbml-file-with-comp-elements.xml');

# We extract one of the species from the model we just read in.
s1 = doc.getModel().getSpecies(0);

# We construct a new model.  This model does not use the 'comp' package.
newDoc = SBMLDocument(3, 1);
newModel = newDoc.createModel();

# The following would fail with an error, because addSpecies() would
# first check that the parent of the given object has namespaces
# declared, and will discover that s1 does but newModel does not.

# newModel.addSpecies(s1);

# However, if we disable the 'comp' package on s1, then the call
# to addSpecies will work.

s1.disablePackage('http://www.sbml.org/sbml/level3/version1/comp/version1',
          'comp');
newModel.addSpecies(s1);
Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
enablePackage()
def libsbml.SBase.enablePackage (   self,
  args 
)
inherited

Python method signature(s):

enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)   int

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package
flagwhether to enable (True) or disable (False) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
disablePackage()
def libsbml.SBase.getAncestorOfType (   self,
  args 
)
inherited

Python method signature(s):

getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase
getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase

Returns the first ancestor object that has the given SBML type code from the given package.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.getAnnotation (   self,
  args 
)
inherited

Python method signature(s):

getAnnotation(SBase self)   XMLNode
getAnnotation(SBase self)   XMLNode

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getAnnotationString (   self,
  args 
)
inherited

Python method signature(s):

getAnnotationString(SBase self)   string
getAnnotationString(SBase self)   string

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getColumn (   self)
inherited

Python method signature(s):

getColumn(SBase self)   long

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getLine()
def libsbml.SBase.getCVTerm (   self,
  args 
)
inherited

Python method signature(s):

getCVTerm(SBase self, long n)   CVTerm

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
def libsbml.SBase.getCVTerms (   self)
inherited

Python method signature(s):

getCVTerms()   CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns the CVTermList for this SBase.

def libsbml.SBaseRef.getElementByMetaId (   self,
  args 
)
inherited

Python method signature(s):

getElementByMetaId(SBaseRef self, string metaid)   SBase

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or None if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
a pointer to the SBase element with the given metaid.
def libsbml.SBaseRef.getElementBySId (   self,
  args 
)
inherited

Python method signature(s):

getElementBySId(SBaseRef self, string id)   SBase

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
a pointer to the SBase element with the given id.
def libsbml.Deletion.getElementName (   self)

Python method signature(s):

getElementName(Deletion self)   string

Returns the XML element name of this SBML object.

Returns
the string of the name of this element.
def libsbml.Deletion.getId (   self)

Python method signature(s):

getId(Deletion self)   string

Returns the value of the 'id' attribute of this Deletion.

Returns
the name of this Deletion.
def libsbml.SBaseRef.getIdRef (   self)
inherited

Python method signature(s):

getIdRef(SBaseRef self)   string

Returns the value of the 'idRef' attribute of this SBaseRef.

Returns
the value of the 'idRef' attribute of this SBaseRef.
def libsbml.SBase.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBase self)   long

Returns the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
def libsbml.SBase.getLine (   self)
inherited

Python method signature(s):

getLine(SBase self)   long

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getColumn()
def libsbml.SBase.getListOfAllElements (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElements(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElements(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns
an SBaseList
def libsbml.SBase.getListOfAllElementsFromPlugins (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElementsFromPlugins(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElementsFromPlugins(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects contained in SBML package plugins.

This method walks down the list of all packages used by the model and returns all objects contained in them.

Returns
an SBaseList of all children objects from plugins.
def libsbml.SBase.getMetaId (   self)
inherited

Python method signature(s):

getMetaId(SBase self)   string

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId()
def libsbml.SBaseRef.getMetaIdRef (   self)
inherited

Python method signature(s):

getMetaIdRef(SBaseRef self)   string

Returns the value of the 'metaIdRef' attribute of this SBaseRef.

Returns
the value of the 'metaIdRef' attribute of this SBaseRef.
def libsbml.SBase.getModel (   self)
inherited

Python method signature(s):

getModel(SBase self)   Model

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()
def libsbml.SBase.getModelHistory (   self,
  args 
)
inherited

Python method signature(s):

getModelHistory(SBase self)   ModelHistory
getModelHistory(SBase self)   ModelHistory

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or None if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Deletion.getName (   self)

Python method signature(s):

getName(Deletion self)   string

Returns the value of the 'name' attribute of this Deletion.

Returns
the name of this Deletion.
def libsbml.SBase.getNamespaces (   self)
inherited

Python method signature(s):

getNamespaces(SBase self)   XMLNamespaces

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Returns
the XML Namespaces associated with this SBML object, or None in certain very usual circumstances where a namespace is not set.
See also
getLevel()
getVersion()
def libsbml.SBase.getNotes (   self,
  args 
)
inherited

Python method signature(s):

getNotes(SBase self)   XMLNode
getNotes(SBase self)   XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNotesString (   self,
  args 
)
inherited

Python method signature(s):

getNotesString(SBase self)   string
getNotesString(SBase self)   string

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNumCVTerms (   self)
inherited

Python method signature(s):

getNumCVTerms(SBase self)   long

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
def libsbml.SBase.getNumPlugins (   self)
inherited

Python method signature(s):

getNumPlugins(SBase self)   long

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
def libsbml.SBaseRef.getNumReferents (   self)
inherited

Python method signature(s):

getNumReferents(SBaseRef self)   int

Returns how many elements are being referred to by this SBaseRef. A valid SBaseRef will have exactly one. Possible referents are portRef, idRef, unitRef, and metaIdRef.

Returns
integer value between 0 and 4: the number of different ways this element points to its referent.
def libsbml.CompBase.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(CompBase self)   string

Returns the package name of this plugin object.

Returns
the package name of this plugin object.
def libsbml.CompBase.getPackageURI (   self)
inherited

{comp}

comp A convenience subclass of “comp” package SBase-derived classes

The CompBase class derives from SBase, and defines a few functions and features common to all SBase-derived classes in the SBML Level 3 Hierarchical Model Composition package (“comp”). Python method signature(s):

getPackageURI(CompBase self)   string

Returns the XML namespace (URI) of the package extension of this object.

Returns
the URI of the package extension of this plugin object.
def libsbml.CompBase.getPackageVersion (   self)
inherited

Python method signature(s):

getPackageVersion(CompBase self)   long

Returns the package version of the package extension of this plugin object.

Returns
the package version of the package extension of this plugin object.
def libsbml.CompBase.getParentModel (   args)
inherited

Python method signature(s):

getParentModel(SBase child)   Model

Returns the Model object to which the referenced child object belongs.

def libsbml.SBase.getParentSBMLObject (   self,
  args 
)
inherited

Python method signature(s):

getParentSBMLObject(SBase self)   SBase
getParentSBMLObject(SBase self)   SBase

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
def libsbml.SBase.getPlugin (   self,
  args 
)
inherited

Python method signature(s):

getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getPlugin(long n)

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:
getPlugin(string package)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
def libsbml.SBaseRef.getPortRef (   self)
inherited

Python method signature(s):

getPortRef(SBaseRef self)   string

Returns the value of the 'portRef' attribute of this SBaseRef.

Returns
the value of the 'portRef' attribute of this SBaseRef.
def libsbml.SBase.getPrefix (   self)
inherited

Python method signature(s):

getPrefix(SBase self)   string

Returns the namespace prefix of this element.

def libsbml.SBaseRef.getReferencedElement (   self)
inherited

Python method signature(s):

getReferencedElement(SBaseRef self)   SBase

Returns the object pointed to by this element. If that element was previously found and set with 'saveReferencedElement', that element is returned; otherwise, 'saveReferencedElement' is called first, and the found element is returned.

def libsbml.SBaseRef.getReferencedElementFrom (   self,
  args 
)
inherited

Python method signature(s):

getReferencedElementFrom(SBaseRef self, Model model)   SBase

Examines the referenced Model for the referenced object, and returns it, if found.

Parameters
modelthe Model in which to look for the object referenced by this SBaseRef.
Returns
the element in the referenced Model to which this SBaseRef refers. If this object references an object in a Submodel, the returned object will be in the instantiated Model in that Submodel.
def libsbml.SBase.getResourceBiologicalQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceBiologicalQualifier(SBase self, string resource)   long

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getResourceModelQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceModelQualifier(SBase self, string resource)   long

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBaseRef.getSBaseRef (   self,
  args 
)
inherited

Python method signature(s):

getSBaseRef(SBaseRef self)   SBaseRef
getSBaseRef(SBaseRef self)   SBaseRef

Get the child sBaseRef of this sBaseRef.

Returns
the SBaseRef child of this SBaseRef, or None if none exists.
def libsbml.SBase.getSBMLDocument (   self,
  args 
)
inherited

Python method signature(s):

getSBMLDocument(SBase self)   SBMLDocument
getSBMLDocument(SBase self)   SBMLDocument

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
def libsbml.SBase.getSBOTerm (   self)
inherited

Python method signature(s):

getSBOTerm(SBase self)   int

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
def libsbml.SBase.getSBOTermAsURL (   self)
inherited

Python method signature(s):

getSBOTermAsURL(SBase self)   string

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.SBase.getSBOTermID (   self)
inherited

Python method signature(s):

getSBOTermID(SBase self)   string

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.Deletion.getTypeCode (   self)

Python method signature(s):

getTypeCode(Deletion self)   int

Returns the libSBML type code of this object instance.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters “SBML_”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_COMP_DELETION
Warning
The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
getElementName()
getPackageName()
def libsbml.SBaseRef.getUnitRef (   self)
inherited

Python method signature(s):

getUnitRef(SBaseRef self)   string

Returns the value of the 'unitRef' attribute of this SBaseRef.

Returns
the value of the 'unitRef' attribute of this SBaseRef.
def libsbml.SBase.getURI (   self)
inherited

Python method signature(s):

getURI(SBase self)   string

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.

Returns
the URI of this element
See also
getSBMLDocument()
getPackageName()
def libsbml.SBase.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBase self)   long

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
def libsbml.SBaseRef.hasRequiredAttributes (   self)
inherited

Python method signature(s):

hasRequiredAttributes(SBaseRef self)   bool

Returns true if getNumReferents() is exactly 1.

Returns
boolean: 'true' if the attributes are correctly set; 'false' if not.
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self)
inherited

Python method signature(s):

hasValidLevelVersionNamespaceCombination(SBase self)   bool
def libsbml.SBase.isPackageEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageURIEnabled()
def libsbml.SBase.isPackageURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageEnabled()
def libsbml.SBase.isPkgEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgURIEnabled()
def libsbml.SBase.isPkgURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgEnabled()
def libsbml.SBase.isSetAnnotation (   self)
inherited

Python method signature(s):

isSetAnnotation(SBase self)   bool

Predicate returning True if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
True if a 'annotation' subelement exists, False otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Deletion.isSetId (   self)

Python method signature(s):

isSetId(Deletion self)   bool

Predicate returning True or False depending on whether this object's 'id' attribute has been set.

Some words of explanation about the set/unset/isSet methods: The SBML specifications define certain attributes on some classes of objects as being optional. This requires an application to be careful about the distinction between two cases when reading a model: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value if one exists, and (2) a given attribute has been set to a value, but the value happens to be an empty string. The situation can be ambiguous when reading a model from a file or data stream and then examining the data objects that libSBML constructs as a result. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.
Returns
True if the 'id' attribute of this object has been set, False otherwise.
def libsbml.SBaseRef.isSetIdRef (   self)
inherited

Python method signature(s):

isSetIdRef(SBaseRef self)   bool

Predicate returning True or False depending on whether this SBaseRef's 'idRef' attribute has been set.

Returns
True if this SBaseRef's 'idRef' attribute has been set, otherwise False is returned.
def libsbml.SBase.isSetMetaId (   self)
inherited

Python method signature(s):

isSetMetaId(SBase self)   bool

Predicate returning True if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
True if the 'metaid' attribute of this SBML object is set, False otherwise.
See also
getMetaId()
setMetaId()
def libsbml.SBaseRef.isSetMetaIdRef (   self)
inherited

Python method signature(s):

isSetMetaIdRef(SBaseRef self)   bool

Predicate returning True or False depending on whether this SBaseRef's 'metaIdRef' attribute has been set.

Returns
True if this SBaseRef's 'metaIdRef' attribute has been set, otherwise False is returned.
def libsbml.SBase.isSetModelHistory (   self)
inherited

Python method signature(s):

isSetModelHistory(SBase self)   bool

Predicate returning True if this object has a ModelHistory object attached to it.

Returns
True if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Deletion.isSetName (   self)

Python method signature(s):

isSetName(Deletion self)   bool

Predicate returning True or False depending on whether this object's 'name' attribute has been set.

Some words of explanation about the set/unset/isSet methods: The SBML specifications define certain attributes on some classes of objects as being optional. This requires an application to be careful about the distinction between two cases when reading a model: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value if one exists, and (2) a given attribute has been set to a value, but the value happens to be an empty string. The situation can be ambiguous when reading a model from a file or data stream and then examining the data objects that libSBML constructs as a result. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.
Returns
True if the 'name' attribute of this object has been set, false otherwise.
def libsbml.SBase.isSetNotes (   self)
inherited

Python method signature(s):

isSetNotes(SBase self)   bool

Predicate returning True if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
True if a 'notes' subelement exists, False otherwise.
See also
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBaseRef.isSetPortRef (   self)
inherited

Python method signature(s):

isSetPortRef(SBaseRef self)   bool

Predicate returning True or False depending on whether this SBaseRef's 'portRef' attribute has been set.

Returns
True if this SBaseRef's 'portRef' attribute has been set, otherwise False is returned.
def libsbml.SBaseRef.isSetSBaseRef (   self)
inherited

Python method signature(s):

isSetSBaseRef(SBaseRef self)   bool

Predicate for testing whether the sBaseRef for this SBaseRef is set.

Returns
True if the sBaseRef of this SBaseRef is set, False otherwise.
def libsbml.SBase.isSetSBOTerm (   self)
inherited

Python method signature(s):

isSetSBOTerm(SBase self)   bool

Predicate returning True if this object's 'sboTerm' attribute is set.

Returns
True if the 'sboTerm' attribute of this SBML object is set, False otherwise.
def libsbml.SBaseRef.isSetUnitRef (   self)
inherited

Python method signature(s):

isSetUnitRef(SBaseRef self)   bool

Predicate returning True or False depending on whether this SBaseRef's 'unitRef' attribute has been set.

Returns
True if this SBaseRef's 'unitRef' attribute has been set, otherwise False is returned.
def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,
  args 
)
inherited

Python method signature(s):

matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.
def libsbml.SBase.matchesSBMLNamespaces (   self,
  args 
)
inherited

Python method signature(s):

matchesSBMLNamespaces(SBase self, SBase sb)   bool
matchesSBMLNamespaces(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is the same as sb's, False otherwise.
def libsbml.SBaseRef.performDeletion (   self)
inherited

Python method signature(s):

performDeletion(SBaseRef self)   int

DEPRECATED FUNCTION: DO NOT USE

Deletes the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children. Instead of calling this function directly, use 'CompModelPlugin::instantiateSubmodels' instead, which deals with all the intricacies of replacements and deletions, and gives you access to the non-flattened hierarchical form of the model.

def libsbml.SBaseRef.removeFromParentAndDelete (   self)
inherited

Python method signature(s):

removeFromParentAndDelete(SBaseRef self)   int

Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.removeTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="", bool removeEmpty=True)   int
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")   int
removeTopLevelAnnotationElement(SBase self, string elementName)   int

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.renameMetaIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameMetaIdRefs(SBase self, string oldid, string newid)

Renames all the meta-identifier attributes on this element.

In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBaseRef.renameSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameSIdRefs(SBaseRef self, string oldid, string newid)

Renames all the SIdRef attributes on this element if they match oldid, but not any found in child or plugin elements.

def libsbml.SBase.renameUnitSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameUnitSIdRefs(SBase self, string oldid, string newid)

Renames all the UnitSIdRef attributes on this element.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.replaceTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)   int
replaceTopLevelAnnotationElement(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
replaceTopLevelAnnotationElement(XMLNode annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()

Method variant with the following signature:
replaceTopLevelAnnotationElement(string annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.Deletion.saveReferencedElement (   self)

Python method signature(s):

saveReferencedElement(Deletion self)   int

Finds and stores the referenced object. It finds its Submodel parent, gets its instantiated Model object, calls 'getReferencedElementFrom' on that model, and stores the result.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.setAnnotation (   self,
  args 
)
inherited

Python method signature(s):

setAnnotation(SBase self, XMLNode annotation)   int
setAnnotation(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setAnnotation(XMLNode annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
setAnnotation(string annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Deletion.setId (   self,
  args 
)

Python method signature(s):

setId(Deletion self, string id)   int

Sets the value of the 'id' attribute of this Deletion.

This method fails if the id is not a valid syntax for an SId.

Parameters
idthe identifier to use
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBaseRef.setIdRef (   self,
  args 
)
inherited

Python method signature(s):

setIdRef(SBaseRef self, string id)   int

Sets the value of the 'idRef' attribute of this SBaseRef.

This method fails if the id is not a valid syntax for an SIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). A sBaseRef must use exactly one method to point to a submodel element.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.setMetaId (   self,
  args 
)
inherited

Python method signature(s):

setMetaId(SBase self, string metaid)   int

Sets the value of the meta-identifier attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
def libsbml.SBaseRef.setMetaIdRef (   self,
  args 
)
inherited

Python method signature(s):

setMetaIdRef(SBaseRef self, string id)   int

Sets the value of the 'metaIdRef' attribute of this SBaseRef.

This method fails if the id is not a valid syntax for an IDREF (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). An sBaseRef must use exactly one method to point to a submodel element.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.setModelHistory (   self,
  args 
)
inherited

Python method signature(s):

setModelHistory(SBase self, ModelHistory history)   int

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Deletion.setName (   self,
  args 
)

Python method signature(s):

setName(Deletion self, string name)   int

Sets the value of the 'name' attribute of this Deletion.

The string in name is copied.

Parameters
namethe new name for the Deletion
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.setNamespaces (   self,
  args 
)
inherited

Python method signature(s):

setNamespaces(SBase self, XMLNamespaces xmlns)   int

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setNotes (   self,
  args 
)
inherited

Python method signature(s):

setNotes(SBase self, XMLNode notes)   int
setNotes(SBase self, string notes, bool addXHTMLMarkup=False)   int
setNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setNotes(string notes, bool addXHTMLMarkup = false)

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
setNotes(XMLNode notes)

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBaseRef.setPortRef (   self,
  args 
)
inherited

Python method signature(s):

setPortRef(SBaseRef self, string id)   int

Sets the value of the 'portRef' attribute of this SBaseRef. Fails if the id is not a valid syntax for a PortSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). An SBaseRef must use exactly one method to point to a submodel element.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBaseRef.setSBaseRef (   self,
  args 
)
inherited

Python method signature(s):

setSBaseRef(SBaseRef self, SBaseRef sBaseRef)   int

Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.

This method fails if the added sBaseRef does not match the level/version/package of the parent object or if the added sBaseRef cannot be copied.

Parameters
sBaseRefthe SBaseRef object instance to use.
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.setSBOTerm (   self,
  args 
)
inherited

Python method signature(s):

setSBOTerm(SBase self, int value)   int
setSBOTerm(SBase self, string sboid)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()

Method variant with the following signature:
setSBOTerm(string &sboid)

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()
def libsbml.SBaseRef.setUnitRef (   self,
  args 
)
inherited

Python method signature(s):

setUnitRef(SBaseRef self, string id)   int

Sets the value of the 'unitRef' attribute of this SBaseRef.

This method fails if the id is not a valid syntax for a UnitSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). A sBaseRef must use exactly one method to point to a submodel element.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.toSBML (   self)
inherited

Python method signature(s):

toSBML(SBase self)   string *

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
def libsbml.SBase.toXMLNode (   self)
inherited

Python method signature(s):

toXMLNode(SBase self)   XMLNode

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
def libsbml.SBase.unsetAnnotation (   self)
inherited

Python method signature(s):

unsetAnnotation(SBase self)   int

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
def libsbml.SBase.unsetCVTerms (   self)
inherited

Python method signature(s):

unsetCVTerms(SBase self)   int

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Deletion.unsetId (   self)

Python method signature(s):

unsetId(Deletion self)   int

Unsets the value of the 'id' attribute of this Deletion.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBaseRef.unsetIdRef (   self)
inherited

Python method signature(s):

unsetIdRef(SBaseRef self)   int

Unsets the value of the 'idRef' attribute of this SBaseRef.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.unsetMetaId (   self)
inherited

Python method signature(s):

unsetMetaId(SBase self)   int

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBaseRef.unsetMetaIdRef (   self)
inherited

Python method signature(s):

unsetMetaIdRef(SBaseRef self)   int

Unsets the value of the 'metaIdRef' attribute of this SBaseRef.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.unsetModelHistory (   self)
inherited

Python method signature(s):

unsetModelHistory(SBase self)   int

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Deletion.unsetName (   self)

Python method signature(s):

unsetName(Deletion self)   int

Unsets the value of the 'name' attribute of this Deletion.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.unsetNotes (   self)
inherited

Python method signature(s):

unsetNotes(SBase self)   int

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBaseRef.unsetPortRef (   self)
inherited

Python method signature(s):

unsetPortRef(SBaseRef self)   int

Unsets the value of the 'portRef' attribute of this SBaseRef.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBaseRef.unsetSBaseRef (   self)
inherited

Python method signature(s):

unsetSBaseRef(SBaseRef self)   int

Unsets the child SBaseRef of this SBaseRef. Deletes the former SBaseRef child, if one existed.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.SBase.unsetSBOTerm (   self)
inherited

Python method signature(s):

unsetSBOTerm(SBase self)   int

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBaseRef.unsetUnitRef (   self)
inherited

Python method signature(s):

unsetUnitRef(SBaseRef self)   int

Unsets the value of the 'unitRef' attribute of this SBaseRef.

Returns
integer value indicating success/failure of the operation. The possible return values are: